GSM5454740: ChIP-seq GC4249 K562 HZdKD CTCF; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
TFs and others
Antigen
CTCF
Cell type
Cell type Class
Blood
Cell type
K-562
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Chronic Myelogenous
Attributes by original data submitter
Sample
source_name
K562
cell line
K562
genotype
ZNF143 HCFC1 double knockdown
chip antibody
CTCF antibody
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Genomic DNA was purified by Phenol-Chloroform extraction. RNA was extracted with QIAzol lysis reagent (QIAGEN) and RNeasy mini kit (QIAGEN). For Hi-TrAC, repair DNA gaps with T4 DNA polymerase. Remove free bridging linker by AMPure XP beads. Then, Digest purified DNA with restriction enzymes MluCI/NlaIII, and enrich biotin-labeled DNA fragments with streptavidin beads. Perform adapter ligation on beads. After washing the beads, run PCR with illumina multiplexing indexed primers. For RNA-seq, libraries were constructed following Smart-seq2 protocol (Picelli et al., 2014). For ChIP-seq, sheared chromatins were immunoprecipitated with anti-CTCF, anti-RAD21, anti-HCFC1, anti-ZNF143 antibodies. DNA was purified, then end-repaired using End-It DNA End-Repair kit (Epicentre). A-tailing was performed with Klenow Fragment (3'->5' exo-) with the presence of dATP. Universal adapters were then ligated. The libraries were then amplified by PCR using indexed primers.